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\name{lastz}
\alias{lastz}
\title{
lastz wrapper
}
\description{
Wrapper function of \command{lastz} to do the pairwise whole genome alignment.
This function doesn't work on Windows platform.
}
\usage{
lastz(assemblyTarget, assemblyQuery, outputDir = ".",
chrsTarget = NULL, chrsQuery = NULL,
distance = c("far", "medium", "near"), binary = "lastz",
mc.cores = getOption("mc.cores", 2L), echoCommand = FALSE)
}
\arguments{
\item{assemblyTarget}{
\code{character}(1): the file name of target assembly \emph{twoBit} file.
}
\item{assemblyQuery}{
\code{character}(1): the file name of query assembly \emph{twoBit} file.
}
\item{outputDir}{
\code{character}(1): the folder to put the generated \emph{lav} files.
}
\item{chrsTarget}{
NULL or \code{character}(n): when it's NULL, all the available chromosomes
from the target assembly will be aligned.
}
\item{chrsQuery}{
NULL or \code{character}(n): when it's NULL, all the available chromosomes
from the query assembly will be aligned.
}
\item{distance}{
It can be "far", "medium" or "near". It decides the score matrix used in
\emph{lastz} aligner.
See `?scoringMatrix` for more details.
}
\item{binary}{
\code{character}(1): the name/filename of the binary \command{lastz} to call.
}
\item{mc.cores}{
\code{integer}(1): the number of threads to use.
By default, \code{getOption("mc.cores", 2L)}.
}
\item{echoCommand}{
\code{boolean}(1): When \code{TRUE},
only the command to run \command{lastz} is returned.
}
}
\value{
A \code{character}(n) vector of ouput \emph{lav} file names.
}
\references{
\url{http://www.bx.psu.edu/~rsharris/lastz/}
}
\author{
Ge Tan
}
\note{
\command{lastz} aligner must be installed on the machine to use this function.
}
\seealso{
\code{\link{lavToPsl}}
}
\examples{
\dontrun{
## This example doesn't run because it requires two bit files and external
## Kent utilities.
assemblyTarget <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/danRer10.2bit"
assemblyQuery <- "/Users/gtan/OneDrive/Project/CSC/CNEr/2bit/hg38.2bit"
lavs <- lastz(assemblyTarget, assemblyQuery,
outputDir="/Users/gtan/OneDrive/Project/CSC/CNEr/axt",
chrsTarget=c("chr1", "chr2", "chr3"),
chrsQuery=c("chr1", "chr2", "chr3"),
distance="far", mc.cores=4)
}
}
|
